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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-03-01, 22:22 EST based on data in: /local/workdir/kah357/Amplicon_Project/analysis/00_FastQC/fastqc_reports


        General Statistics

        Showing 416/416 rows and 3/6 columns.
        Sample Name% Dups% GCM Seqs
        ERR3141386_1
        89.6%
        53%
        0.2
        ERR3141386_2
        87.3%
        50%
        0.2
        ERR3141387_1
        88.6%
        54%
        0.2
        ERR3141387_2
        90.0%
        52%
        0.2
        ERR3141388_1
        93.6%
        53%
        0.4
        ERR3141388_2
        93.3%
        50%
        0.4
        ERR3141389_1
        93.3%
        54%
        0.2
        ERR3141389_2
        94.1%
        51%
        0.2
        ERR3141390_1
        87.1%
        51%
        0.3
        ERR3141390_2
        87.8%
        50%
        0.3
        ERR3141391_1
        90.3%
        53%
        0.1
        ERR3141391_2
        92.1%
        52%
        0.1
        ERR3141392_1
        90.3%
        52%
        0.2
        ERR3141392_2
        90.6%
        50%
        0.2
        ERR3141393_1
        90.4%
        54%
        0.2
        ERR3141393_2
        91.1%
        52%
        0.2
        ERR3141394_1
        91.0%
        54%
        0.5
        ERR3141394_2
        90.4%
        51%
        0.5
        ERR3141395_1
        88.8%
        53%
        0.2
        ERR3141395_2
        90.5%
        52%
        0.2
        ERR3141396_1
        89.5%
        53%
        0.3
        ERR3141396_2
        91.0%
        51%
        0.3
        ERR3141397_1
        91.1%
        53%
        0.1
        ERR3141397_2
        88.2%
        51%
        0.1
        ERR3141398_1
        88.3%
        53%
        0.2
        ERR3141398_2
        90.2%
        51%
        0.2
        ERR3141399_1
        88.1%
        53%
        0.2
        ERR3141399_2
        84.4%
        51%
        0.2
        ERR3141400_1
        85.2%
        52%
        0.1
        ERR3141400_2
        83.7%
        50%
        0.1
        ERR3141401_1
        92.9%
        53%
        0.1
        ERR3141401_2
        87.7%
        50%
        0.1
        ERR3141402_1
        84.2%
        52%
        0.1
        ERR3141402_2
        83.8%
        51%
        0.1
        ERR3141403_1
        88.6%
        53%
        0.1
        ERR3141403_2
        85.8%
        51%
        0.1
        ERR3141404_1
        86.5%
        52%
        0.1
        ERR3141404_2
        86.2%
        50%
        0.1
        ERR3141405_1
        89.4%
        52%
        0.3
        ERR3141405_2
        88.5%
        50%
        0.3
        ERR3141406_1
        90.2%
        54%
        0.2
        ERR3141406_2
        91.1%
        52%
        0.2
        ERR3141407_1
        90.9%
        53%
        0.3
        ERR3141407_2
        89.7%
        51%
        0.3
        ERR3141408_1
        88.3%
        53%
        0.1
        ERR3141408_2
        88.9%
        51%
        0.1
        ERR3141409_1
        91.3%
        54%
        0.4
        ERR3141409_2
        91.3%
        52%
        0.4
        ERR3141410_1
        91.0%
        53%
        0.3
        ERR3141410_2
        90.7%
        51%
        0.3
        ERR3141411_1
        88.8%
        53%
        0.2
        ERR3141411_2
        90.3%
        51%
        0.2
        ERR3141412_1
        89.0%
        53%
        0.2
        ERR3141412_2
        88.2%
        51%
        0.2
        ERR3141413_1
        86.7%
        53%
        0.1
        ERR3141413_2
        87.3%
        52%
        0.1
        ERR3141414_1
        89.3%
        54%
        0.2
        ERR3141414_2
        87.9%
        52%
        0.2
        ERR3141415_1
        85.7%
        53%
        0.1
        ERR3141415_2
        86.0%
        51%
        0.1
        ERR3141416_1
        87.3%
        53%
        0.2
        ERR3141416_2
        86.0%
        51%
        0.2
        ERR3141417_1
        89.8%
        52%
        0.2
        ERR3141417_2
        90.6%
        50%
        0.2
        ERR3141418_1
        93.2%
        53%
        0.2
        ERR3141418_2
        93.2%
        50%
        0.2
        ERR3141419_1
        91.6%
        52%
        0.3
        ERR3141419_2
        88.6%
        51%
        0.3
        ERR3141420_1
        87.0%
        53%
        0.2
        ERR3141420_2
        88.3%
        51%
        0.2
        ERR3141421_1
        93.1%
        53%
        0.1
        ERR3141421_2
        93.2%
        48%
        0.1
        ERR3141422_1
        87.9%
        53%
        0.1
        ERR3141422_2
        90.2%
        51%
        0.1
        ERR3141423_1
        86.6%
        53%
        0.2
        ERR3141423_2
        88.0%
        51%
        0.2
        ERR3141424_1
        87.2%
        53%
        0.2
        ERR3141424_2
        89.1%
        51%
        0.2
        ERR3141425_1
        89.0%
        53%
        0.2
        ERR3141425_2
        90.4%
        51%
        0.2
        ERR3141426_1
        91.1%
        54%
        0.2
        ERR3141426_2
        91.9%
        52%
        0.2
        ERR3141427_1
        89.0%
        53%
        0.1
        ERR3141427_2
        90.5%
        52%
        0.1
        ERR3141428_1
        90.2%
        54%
        0.2
        ERR3141428_2
        91.8%
        51%
        0.2
        ERR3141429_1
        89.7%
        54%
        0.2
        ERR3141429_2
        90.4%
        51%
        0.2
        ERR3141430_1
        89.1%
        53%
        0.1
        ERR3141430_2
        89.9%
        50%
        0.1
        ERR3141431_1
        88.4%
        53%
        0.2
        ERR3141431_2
        89.5%
        51%
        0.2
        ERR3141432_1
        86.0%
        53%
        0.1
        ERR3141432_2
        83.5%
        51%
        0.1
        ERR3141433_1
        84.9%
        53%
        0.1
        ERR3141433_2
        84.0%
        51%
        0.1
        ERR3141434_1
        83.1%
        52%
        0.1
        ERR3141434_2
        79.3%
        50%
        0.1
        ERR3141435_1
        85.4%
        52%
        0.1
        ERR3141435_2
        85.2%
        51%
        0.1
        ERR3141436_1
        89.7%
        54%
        0.1
        ERR3141436_2
        86.2%
        51%
        0.1
        ERR3141437_1
        88.6%
        53%
        0.1
        ERR3141437_2
        87.3%
        51%
        0.1
        ERR3141438_1
        91.0%
        54%
        0.5
        ERR3141438_2
        91.4%
        51%
        0.5
        ERR3141439_1
        90.2%
        53%
        0.2
        ERR3141439_2
        91.0%
        51%
        0.2
        ERR3141440_1
        89.6%
        53%
        0.2
        ERR3141440_2
        90.2%
        51%
        0.2
        ERR3141441_1
        90.1%
        54%
        0.4
        ERR3141441_2
        88.9%
        52%
        0.4
        ERR3141442_1
        87.7%
        52%
        0.2
        ERR3141442_2
        87.8%
        50%
        0.2
        ERR3141443_1
        88.6%
        54%
        0.2
        ERR3141443_2
        90.2%
        52%
        0.2
        ERR3141444_1
        90.1%
        53%
        0.3
        ERR3141444_2
        90.0%
        51%
        0.3
        ERR3141445_1
        88.0%
        52%
        0.2
        ERR3141445_2
        89.5%
        50%
        0.2
        ERR3141446_1
        90.0%
        52%
        0.5
        ERR3141446_2
        90.8%
        50%
        0.5
        ERR3141447_1
        87.9%
        54%
        0.2
        ERR3141447_2
        89.6%
        52%
        0.2
        ERR3141448_1
        87.3%
        53%
        0.3
        ERR3141448_2
        86.4%
        51%
        0.3
        ERR3141449_1
        88.2%
        53%
        0.3
        ERR3141449_2
        90.0%
        51%
        0.3
        ERR3141450_1
        88.1%
        54%
        0.2
        ERR3141450_2
        88.9%
        52%
        0.2
        ERR3141451_1
        91.8%
        54%
        0.3
        ERR3141451_2
        92.2%
        52%
        0.3
        ERR3141452_1
        90.5%
        55%
        0.2
        ERR3141452_2
        91.8%
        53%
        0.2
        ERR3141453_1
        91.1%
        52%
        0.2
        ERR3141453_2
        91.6%
        50%
        0.2
        ERR3141454_1
        82.3%
        54%
        0.1
        ERR3141454_2
        77.8%
        53%
        0.1
        ERR3141455_1
        89.9%
        53%
        0.4
        ERR3141455_2
        88.8%
        51%
        0.4
        ERR3141456_1
        89.6%
        53%
        0.3
        ERR3141456_2
        91.2%
        51%
        0.3
        ERR3141457_1
        88.4%
        52%
        0.3
        ERR3141457_2
        89.4%
        50%
        0.3
        ERR3141458_1
        88.5%
        53%
        0.2
        ERR3141458_2
        89.9%
        51%
        0.2
        ERR3141459_1
        87.4%
        52%
        0.1
        ERR3141459_2
        88.3%
        51%
        0.1
        ERR3141460_1
        89.0%
        53%
        0.2
        ERR3141460_2
        90.0%
        50%
        0.2
        ERR3141461_1
        92.5%
        53%
        0.2
        ERR3141461_2
        92.2%
        49%
        0.2
        ERR3141462_1
        88.3%
        54%
        0.1
        ERR3141462_2
        89.7%
        52%
        0.1
        ERR3141463_1
        91.5%
        53%
        0.2
        ERR3141463_2
        90.3%
        49%
        0.2
        ERR3141464_1
        94.7%
        61%
        0.2
        ERR3141464_2
        94.8%
        57%
        0.2
        ERR3141465_1
        94.4%
        61%
        0.2
        ERR3141465_2
        94.5%
        57%
        0.2
        ERR3141466_1
        93.7%
        61%
        0.1
        ERR3141466_2
        92.9%
        57%
        0.1
        ERR3141467_1
        95.1%
        61%
        0.2
        ERR3141467_2
        94.0%
        58%
        0.2
        ERR3141468_1
        94.2%
        61%
        0.1
        ERR3141468_2
        93.6%
        57%
        0.1
        ERR3141469_1
        94.9%
        61%
        0.1
        ERR3141469_2
        93.9%
        58%
        0.1
        ERR3141470_1
        93.6%
        61%
        0.1
        ERR3141470_2
        91.0%
        57%
        0.1
        ERR3141471_1
        94.6%
        61%
        0.2
        ERR3141471_2
        94.2%
        57%
        0.2
        ERR3141472_1
        94.6%
        62%
        0.2
        ERR3141472_2
        94.2%
        58%
        0.2
        ERR3141473_1
        94.8%
        61%
        0.1
        ERR3141473_2
        94.8%
        57%
        0.1
        ERR3141474_1
        93.5%
        61%
        0.2
        ERR3141474_2
        94.7%
        57%
        0.2
        ERR3141475_1
        94.4%
        61%
        0.2
        ERR3141475_2
        94.8%
        57%
        0.2
        ERR3141476_1
        93.8%
        61%
        0.2
        ERR3141476_2
        92.8%
        57%
        0.2
        ERR3141477_1
        94.2%
        61%
        0.2
        ERR3141477_2
        95.0%
        57%
        0.2
        ERR3141478_1
        94.8%
        61%
        0.2
        ERR3141478_2
        95.0%
        57%
        0.2
        ERR3141479_1
        93.4%
        61%
        0.2
        ERR3141479_2
        94.7%
        57%
        0.2
        ERR3141480_1
        92.4%
        60%
        0.2
        ERR3141480_2
        93.5%
        56%
        0.2
        ERR3141481_1
        94.0%
        61%
        0.2
        ERR3141481_2
        94.5%
        57%
        0.2
        ERR3141482_1
        88.7%
        53%
        0.2
        ERR3141482_2
        89.4%
        50%
        0.2
        ERR3141483_1
        87.5%
        53%
        0.1
        ERR3141483_2
        87.9%
        50%
        0.1
        ERR3141484_1
        94.1%
        53%
        0.3
        ERR3141484_2
        94.4%
        50%
        0.3
        ERR3141485_1
        94.5%
        53%
        0.2
        ERR3141485_2
        94.5%
        50%
        0.2
        ERR3141486_1
        88.1%
        54%
        0.2
        ERR3141486_2
        89.3%
        52%
        0.2
        ERR3141487_1
        89.6%
        54%
        0.3
        ERR3141487_2
        89.7%
        52%
        0.3
        ERR3141488_1
        88.6%
        55%
        0.1
        ERR3141488_2
        88.4%
        53%
        0.1
        ERR3141489_1
        87.0%
        54%
        0.1
        ERR3141489_2
        83.8%
        52%
        0.1
        ERR3141490_1
        87.2%
        53%
        0.1
        ERR3141490_2
        87.4%
        51%
        0.1
        ERR3141491_1
        87.1%
        53%
        0.2
        ERR3141491_2
        87.5%
        51%
        0.2
        ERR3141492_1
        91.2%
        53%
        0.3
        ERR3141492_2
        90.7%
        51%
        0.3
        ERR3141493_1
        90.7%
        54%
        0.2
        ERR3141493_2
        90.5%
        52%
        0.2
        ERR3141494_1
        88.0%
        55%
        0.2
        ERR3141494_2
        87.4%
        53%
        0.2
        ERR3141495_1
        87.4%
        52%
        0.2
        ERR3141495_2
        86.6%
        51%
        0.2
        ERR3141496_1
        86.9%
        54%
        0.1
        ERR3141496_2
        83.1%
        52%
        0.1
        ERR3141497_1
        90.0%
        55%
        0.2
        ERR3141497_2
        90.2%
        53%
        0.2
        ERR3141498_1
        88.6%
        54%
        0.2
        ERR3141498_2
        88.2%
        52%
        0.2
        ERR3141499_1
        91.4%
        55%
        0.2
        ERR3141499_2
        91.2%
        52%
        0.2
        ERR3141500_1
        88.4%
        54%
        0.2
        ERR3141500_2
        89.6%
        52%
        0.2
        ERR3141501_1
        93.0%
        54%
        0.1
        ERR3141501_2
        78.0%
        50%
        0.1
        ERR3141502_1
        89.6%
        54%
        0.1
        ERR3141502_2
        90.6%
        52%
        0.1
        ERR3141503_1
        87.5%
        55%
        0.1
        ERR3141503_2
        86.1%
        53%
        0.1
        ERR3141504_1
        93.2%
        53%
        0.1
        ERR3141504_2
        91.1%
        50%
        0.1
        ERR3141505_1
        87.9%
        52%
        0.2
        ERR3141505_2
        88.1%
        50%
        0.2
        ERR3141506_1
        91.2%
        53%
        0.1
        ERR3141506_2
        91.9%
        52%
        0.1
        ERR3141507_1
        92.5%
        53%
        0.2
        ERR3141507_2
        92.8%
        51%
        0.2
        ERR3141508_1
        89.6%
        54%
        0.2
        ERR3141508_2
        90.1%
        53%
        0.2
        ERR3141509_1
        92.3%
        54%
        0.2
        ERR3141509_2
        91.5%
        53%
        0.2
        ERR3141510_1
        91.0%
        55%
        0.3
        ERR3141510_2
        91.3%
        53%
        0.3
        ERR3141511_1
        90.0%
        54%
        0.2
        ERR3141511_2
        89.7%
        52%
        0.2
        ERR3141512_1
        88.1%
        53%
        0.1
        ERR3141512_2
        86.1%
        51%
        0.1
        ERR3141513_1
        90.8%
        54%
        0.2
        ERR3141513_2
        91.4%
        52%
        0.2
        ERR3141514_1
        89.2%
        55%
        0.2
        ERR3141514_2
        90.1%
        53%
        0.2
        ERR3141515_1
        87.7%
        53%
        0.2
        ERR3141515_2
        88.0%
        51%
        0.2
        ERR3141516_1
        89.1%
        53%
        0.2
        ERR3141516_2
        89.0%
        51%
        0.2
        ERR3141517_1
        88.0%
        53%
        0.2
        ERR3141517_2
        88.0%
        51%
        0.2
        ERR3141518_1
        89.6%
        54%
        0.2
        ERR3141518_2
        90.1%
        52%
        0.2
        ERR3141519_1
        90.7%
        54%
        0.1
        ERR3141519_2
        90.8%
        52%
        0.1
        ERR3141520_1
        85.9%
        54%
        0.1
        ERR3141520_2
        84.8%
        52%
        0.1
        ERR3141521_1
        89.3%
        54%
        0.3
        ERR3141521_2
        90.1%
        52%
        0.3
        ERR3141522_1
        87.7%
        55%
        0.2
        ERR3141522_2
        89.0%
        53%
        0.2
        ERR3141523_1
        89.2%
        54%
        0.2
        ERR3141523_2
        90.4%
        52%
        0.2
        ERR3141524_1
        90.2%
        54%
        0.2
        ERR3141524_2
        89.7%
        52%
        0.2
        ERR3141525_1
        90.9%
        54%
        0.3
        ERR3141525_2
        91.7%
        52%
        0.3
        ERR3141526_1
        89.9%
        54%
        0.2
        ERR3141526_2
        90.8%
        52%
        0.2
        ERR3141527_1
        86.5%
        54%
        0.1
        ERR3141527_2
        85.4%
        52%
        0.1
        ERR3141528_1
        88.3%
        54%
        0.2
        ERR3141528_2
        89.5%
        52%
        0.2
        ERR3141529_1
        88.2%
        54%
        0.2
        ERR3141529_2
        88.6%
        52%
        0.2
        ERR3141530_1
        87.4%
        54%
        0.2
        ERR3141530_2
        85.5%
        52%
        0.2
        ERR3141531_1
        87.8%
        53%
        0.2
        ERR3141531_2
        89.0%
        51%
        0.2
        ERR3141532_1
        89.1%
        54%
        0.1
        ERR3141532_2
        89.8%
        52%
        0.1
        ERR3141533_1
        90.3%
        54%
        0.3
        ERR3141533_2
        91.2%
        53%
        0.3
        ERR3141534_1
        88.0%
        53%
        0.2
        ERR3141534_2
        87.5%
        52%
        0.2
        ERR3141535_1
        87.3%
        54%
        0.1
        ERR3141535_2
        84.5%
        53%
        0.1
        ERR3141536_1
        87.8%
        53%
        0.2
        ERR3141536_2
        87.4%
        52%
        0.2
        ERR3141537_1
        84.7%
        53%
        0.1
        ERR3141537_2
        84.6%
        51%
        0.1
        ERR3141538_1
        86.9%
        54%
        0.1
        ERR3141538_2
        88.3%
        52%
        0.1
        ERR3141539_1
        87.6%
        54%
        0.1
        ERR3141539_2
        88.4%
        52%
        0.1
        ERR3141540_1
        89.2%
        53%
        0.1
        ERR3141540_2
        89.7%
        51%
        0.1
        ERR3141541_1
        87.6%
        54%
        0.2
        ERR3141541_2
        88.8%
        52%
        0.2
        ERR3141542_1
        88.1%
        54%
        0.2
        ERR3141542_2
        87.7%
        52%
        0.2
        ERR3141543_1
        86.6%
        54%
        0.1
        ERR3141543_2
        85.1%
        53%
        0.1
        ERR3141544_1
        88.6%
        54%
        0.2
        ERR3141544_2
        89.3%
        53%
        0.2
        ERR3141545_1
        87.3%
        54%
        0.1
        ERR3141545_2
        88.4%
        52%
        0.1
        ERR3141546_1
        85.9%
        55%
        0.1
        ERR3141546_2
        83.7%
        53%
        0.1
        ERR3141547_1
        89.5%
        55%
        0.2
        ERR3141547_2
        89.5%
        53%
        0.2
        ERR3141548_1
        87.4%
        55%
        0.2
        ERR3141548_2
        87.9%
        53%
        0.2
        ERR3141549_1
        89.5%
        55%
        0.2
        ERR3141549_2
        89.5%
        53%
        0.2
        ERR3141550_1
        89.7%
        55%
        0.2
        ERR3141550_2
        90.8%
        52%
        0.2
        ERR3141551_1
        86.3%
        53%
        0.1
        ERR3141551_2
        87.2%
        51%
        0.1
        ERR3141552_1
        91.1%
        55%
        0.1
        ERR3141552_2
        90.7%
        52%
        0.1
        ERR3141553_1
        91.6%
        54%
        0.2
        ERR3141553_2
        90.5%
        52%
        0.2
        ERR3141554_1
        92.2%
        53%
        0.1
        ERR3141554_2
        90.6%
        51%
        0.1
        ERR3141555_1
        94.4%
        53%
        0.3
        ERR3141555_2
        94.2%
        50%
        0.3
        ERR3141556_1
        89.2%
        53%
        0.1
        ERR3141556_2
        87.0%
        51%
        0.1
        ERR3141557_1
        95.8%
        53%
        0.2
        ERR3141557_2
        95.6%
        49%
        0.2
        ERR3141558_1
        93.4%
        53%
        0.2
        ERR3141558_2
        93.6%
        51%
        0.2
        ERR3141559_1
        90.9%
        53%
        0.2
        ERR3141559_2
        91.2%
        51%
        0.2
        ERR3141560_1
        88.5%
        54%
        0.1
        ERR3141560_2
        86.7%
        52%
        0.1
        ERR3141561_1
        95.2%
        53%
        0.2
        ERR3141561_2
        95.1%
        49%
        0.2
        ERR3141562_1
        90.0%
        53%
        0.2
        ERR3141562_2
        91.2%
        51%
        0.2
        ERR3141563_1
        91.7%
        54%
        0.2
        ERR3141563_2
        91.7%
        51%
        0.2
        ERR3141564_1
        92.7%
        54%
        0.2
        ERR3141564_2
        92.9%
        51%
        0.2
        ERR3141565_1
        93.3%
        54%
        0.2
        ERR3141565_2
        91.0%
        52%
        0.2
        ERR3141566_1
        94.2%
        53%
        0.2
        ERR3141566_2
        93.2%
        51%
        0.2
        ERR3141567_1
        93.1%
        53%
        0.1
        ERR3141567_2
        92.1%
        51%
        0.1
        ERR3141568_1
        93.4%
        53%
        0.2
        ERR3141568_2
        92.1%
        51%
        0.2
        ERR3141569_1
        94.2%
        53%
        0.2
        ERR3141569_2
        93.2%
        51%
        0.2
        ERR3141570_1
        94.3%
        54%
        0.3
        ERR3141570_2
        93.9%
        52%
        0.3
        ERR3141571_1
        93.3%
        54%
        0.2
        ERR3141571_2
        93.4%
        51%
        0.2
        ERR3141572_1
        94.5%
        53%
        0.2
        ERR3141572_2
        94.2%
        51%
        0.2
        ERR3141573_1
        91.7%
        54%
        0.1
        ERR3141573_2
        89.3%
        51%
        0.1
        ERR3141574_1
        94.0%
        52%
        0.1
        ERR3141574_2
        93.1%
        51%
        0.1
        ERR3141575_1
        92.8%
        52%
        0.1
        ERR3141575_2
        92.1%
        51%
        0.1
        ERR3141576_1
        93.9%
        53%
        0.2
        ERR3141576_2
        93.4%
        50%
        0.2
        ERR3141577_1
        94.6%
        53%
        0.2
        ERR3141577_2
        94.6%
        50%
        0.2
        ERR3143460_1
        13.7%
        45%
        0.9
        ERR3143460_2
        12.7%
        45%
        0.9
        ERR3143461_1
        13.6%
        45%
        1.1
        ERR3143461_2
        12.9%
        45%
        1.1
        ERR3143462_1
        13.2%
        45%
        0.8
        ERR3143462_2
        11.3%
        45%
        0.8
        ERR3143463_1
        13.8%
        45%
        0.8
        ERR3143463_2
        12.8%
        45%
        0.8
        ERR3143464_1
        12.7%
        44%
        0.9
        ERR3143464_2
        12.3%
        44%
        0.9
        ERR3143465_1
        11.9%
        44%
        0.8
        ERR3143465_2
        12.0%
        44%
        0.8
        ERR3143466_1
        11.9%
        44%
        0.8
        ERR3143466_2
        11.2%
        44%
        0.8
        ERR3143467_1
        13.0%
        45%
        0.9
        ERR3143467_2
        13.0%
        45%
        0.9
        ERR3143468_1
        14.5%
        45%
        0.9
        ERR3143468_2
        13.9%
        45%
        0.9
        ERR3143469_1
        13.3%
        45%
        1.0
        ERR3143469_2
        13.5%
        45%
        1.0
        ERR3143470_1
        12.2%
        45%
        0.8
        ERR3143470_2
        11.3%
        45%
        0.8
        ERR3143471_1
        15.9%
        46%
        1.1
        ERR3143471_2
        16.0%
        46%
        1.1
        ERR3143472_1
        14.0%
        45%
        1.0
        ERR3143472_2
        13.6%
        45%
        1.0
        ERR3143473_1
        25.7%
        48%
        1.0
        ERR3143473_2
        25.5%
        48%
        1.0
        ERR3143474_1
        19.9%
        47%
        0.7
        ERR3143474_2
        18.6%
        47%
        0.7
        ERR3143475_1
        17.1%
        46%
        1.0
        ERR3143475_2
        16.9%
        46%
        1.0

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        All samples have sequences of a single length (251bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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